always output the SU alignment

Author: HuaiyanRen

main/phyloanalysis.cpp

@@ -6319,6 +6319,10 @@ void runModelTamerAnalysis(Params &params, Checkpoint *checkpoint) {
         delete orig_aln;
     }
 
+    // write SU alignment to file
+    string su_file = (string)params.out_prefix + ".su_aln.phy";
+    alignment->printAlignment(IN_PHYLIP, su_file.c_str());
+
     runPhyloAnalysis(params, checkpoint, tree, alignment, true);
     alignment = tree->aln;
     delete tree;